We report on Scanning Thermal Lithography (SThL), a recently introduced lithographic tool, for local thermochemistry on tert-butyl acrylate based polymer films featuring chemical cross links. The tailored polymer films afford platforms for controlled high molecular density coupling and surface immobilization of biologically relevant molecules, such as proteins. The thermally labile tert-butyl ester groups in tert-butyl acrylate based polymer films can be cleaved in air at temperatures above 150 °C to yield carboxylic acid functional groups for further (bio)- conjugation. The films were optimized to avoid plastic deformation at the elevated temperatures used during SThL. Exploiting these properties patterns with length scales as small as 35 ± 6 nm have been successfully thermally activated with SThL. Hence SThL comprises an attractive approach for the development of e.g. (bio)sensors and platforms for cell surface interaction studies with nanoscale patterns.